Single Open Reading Frame Research Articles

Transposition of IS4 Family Insertion Sequences ISTeha3, ISTeha4, and ISTeha5 into the arc Operon Disrupts Arginine Deiminase System in Tetragenococcus halophilus.

Tetragenococcus halophilus, a halophilic lactic acid bacterium, is often used as a starter culture in the manufacturing of soy sauce. T. halophilus possesses an arginine deiminase system, which is responsible for the accumulation of citrulline, the main precursor of the potential carcinogen ethyl carbamate. In this study, we generated five derivatives lacking arginine deiminase activity from T. halophilus NBRC 12172 by UV irradiation. Using these derivatives as a fermentation starter prevented arginine deimination in soy sauce. DNA sequence analysis of the derivatives revealed that novel IS4 family insertion sequences, designated ISTeha3, ISTeha4, and ISTeha5, were transposed into the region around the arginine deiminase (arc) operon in the mutants. These insertion sequences contain a single open reading frame encoding a putative transposase and 13- to 15-bp inverted repeats at both termini, which are adjacent to 7- to 9-bp duplications of the target sequence. Investigation of wild strains isolated from soy sauce mash incapable of arginine deimination also indicated that insertion sequences are involved in the disruption of the arginine deiminase system in T. halophilusIMPORTANCE Insertion sequences play important roles in bacterial evolution and are frequently utilized in mutagenesis systems. However, the intrinsic insertion sequences of tetragenococci are not well characterized. Here, we identified three active insertion sequences of T. halophilus by transposition into the region around the arc operon. This report provides an example of insertion sequence-mediated generation and evolution of T. halophilus and primary information about their characteristics.

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames.

Genome annotation is central to today's proteomic research as it draws the outlines of the proteomic landscape. Traditional models of open reading frame (ORF) annotation impose two arbitrary criteria: a minimum length of 100 codons and a single ORF per transcript. However, a growing number of studies report expression of proteins from allegedly non-coding regions, challenging the accuracy of current genome annotations. These novel proteins were found encoded either within non-coding RNAs, 5' or 3' untranslated regions (UTRs) of mRNAs, or overlapping a known coding sequence (CDS) in an alternative ORF. OpenProt is the first database that enforces a polycistronic model for eukaryotic genomes, allowing annotation of multiple ORFs per transcript. OpenProt is freely accessible and offers custom downloads of protein sequences across 10 species. Using OpenProt database for proteomic experiments enables novel proteins discovery and highlights the polycistronic nature of eukaryotic genes. The size of OpenProt database (all predicted proteins) is substantial and need be taken in account for the analysis. However, with appropriate false discovery rate (FDR) settings or the use of a restricted OpenProt database, users will gain a more realistic view of the proteomic landscape. Overall, OpenProt is a freely available tool that will foster proteomic discoveries.

Molecular Characterization of a Debilitation-Associated Partitivirus Infecting the Pathogenic Fungus Aspergillus flavus.

The opportunistic human pathogenic fungus Aspergillus flavus is known to be infected with mycoviruses. In this study, we report a novel mycovirus A. flavus partitivirus 1 (AfPV1) that was originally isolated from the abnormal colonial morphology isolate LD-3-8 of A. flavus. AfPV1 has spherical virus-like particles about 40 nm in diameter, and three double-stranded RNA (dsRNA) segments (dsRNA1, 2, and 3 with lengths of 1.7, 1.4, and 1.1 kbp, respectively) were packaged in the virions. dsRNA1, dsRNA2, and dsRNA3 each contained a single open reading frame and potentially encoded 62, 42, and 32 kDa proteins, respectively. The dsRNA1 encoded protein shows similarity to the RNA-dependent RNA polymerase (RdRp) of partitiviruses, and the dsRNA2 product has no significant similarity to any other capsid protein (CP) in the GenBank databases, beside some homology with the hypothetical “capsid” protein of a few partitiviruses. The dsRNA3 encodes a protein with no similarity to any protein in the GenBank database. SDS-PAGE and polypeptide mass fingerprint-mass spectrum (PMF-MS) analyses indicated that the CP of the AfPV1 was encoded by dsRNA2. Phylogenetic analysis showed that the AfPV1 and relative viruses were found in an unclassified group inside the Partitiviridae family. AfPV1 seems to result in debilitation symptoms, but had no significant effects to murine pathogenicity. These findings provide new insights into the partitiviruses taxonomy and the interactions between viruses and A. flavus.

Biological and molecular characterization of two Anticarsia gemmatalis multiple nucleopolyhedrovirus clones exhibiting contrasting virulence

Baculovirus natural populations are known to be genetically heterogeneous and such genotypic diversity could have implications in the performance of biocontrol agents. The Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV) has been widely used to control the velvetbean caterpillar, Anticarsia gemmatalis, in Brazil. In the present work, morphological and molecular analyses as well as the biological activity of AgMNPV genotypes derived from a Brazilian field isolate (AgMNPV-79) were carried out. The existence of genotypic variants in the population was confirmed by DNA restriction analysis. Although difference in virulence was observed among the variants, the most (Ag79-01) and the least (AgL-16) virulent clones do not show any morphological and cytopathological changes when compared to the most studied isolate (AgMNPV-2D). The complete genome analysis of the two viral clones showed the presence of single open reading frames (ORFs) of the pe-38 and he65 genes, which contrasts with the two split ORFs present in the genome of the AgMNPV-2D isolate. The viral clone AgL-16 has many variations in the ie-2 and pe-38 genes, which are transcription regulatory genes responsible for the regulation of viral early gene expression during insect cell infection. Furthermore, other genes showed alterations like the odv-e56, which have an essential role in the maturation and envelopment of the ODVs, and bro-a and bro-b genes which were fused to form a single ORF. For the Ag79-01, although the total number of single nucleotide variants (SNVs) was more prominent in the pe-38 gene, its genome showed very few modifications in comparison to the AgMNPV-2D genome.

Characterization of a Novel Ourmia-Like Mycovirus Infecting Magnaporthe oryzae and Implications for Viral Diversity and Evolution.

Here, the molecular characterization of a novel mycovirus that was isolated from a phytopathogenic fungus Magnaporthe oryzae and designed as Magnaporthe oryzae ourmia-like virus 4 (MOLV4) is reported. MOLV4 has a genome that is 2497 bp long and possesses a single open reading frame (ORF), which encodes the product RNA-dependent RNA polymerase (RdRp). Sequence similarities were found between the MOLV4 encoded RdRp and the counterparts of a few previously reported ourmia-like mycoviruses. Virus-curing and biological comparison indicate that the virus has no or mild effects on the morphology and mycelium growth rate of the host fungus. Phylogenetic analysis using the RdRp aa sequences was performed. The results show that MOLV4 is clustered with the ourmia-like mycoviruses, forming a clade closely related to ourmiaviruses but distinct from narnaviruses. In addition, database searches revealed that several MOLV4-related sequences are present in the transcriptome shotgun assembly (TSA) library, expressed sequence tag database (ESTdb), whole-genome shotgun (WGS) library, and genomic survey sequences (GSS) libraries of a few other species of eukaryote organisms. Our results show that MOLV4, together with other similar ourmia-like mycoviruses, might represent a virus clade that links the plant ourmiaviruses and fungal narnaviruses and has a wide range of hosts.

A novel enterovirus protein modulates infection in gut epithelial cells

Enteroviruses comprise a large group of mammalian pathogens that includes poliovirus. Pathology in humans ranges from sub-clinical to acute flaccid paralysis, myocarditis and meningitis. Until now, all the enteroviral proteins were thought to derive from proteolytic processing of a polyprotein encoded in a single open reading frame (ORF). We report that many enterovirus genomes also harbor an upstream ORF (uORF) that is subject to strong purifying selection. Using echovirus 7 and poliovirus 1, we confirmed expression of uORF protein (UP) in infected cells. Using ribosome profiling (a technique for global footprinting of translating ribosomes), we also demonstrated translation of the uORF in representative members of the predominant human enterovirus species, namely Enterovirus A, B and C. In differentiated human intestinal organoids, UP-knockout echoviruses are attenuated compared to wild-type virus at late stages of infection where membrane-associated UP facilitates virus release. Thus we have identified a previously unknown enterovirus protein that facilitates virus growth in gut epithelial cells – the site of initial viral invasion into susceptible hosts. These findings overturn the 50-year-old dogma that enteroviruses use a single-polyprotein gene expression strategy, and have important implications for understanding enterovirus pathogenesis.

Studying a mycovirus from Dothistroma septosporum, causative agent of pine needle blight

Dothistroma needle blight caused by D. septosporum has emerged in the British Isles as a major threat to Corsican pine, lodgepole pine and Scots pine. There is increasing evidence that mycoviruses can reduce the growth and pathogenicity of fungal plant pathogens. The aim of the present study is to characterise a double-stranded RNA virus found in D. septosporum and investigatefor putative hypovirulence, a common feature noted for mycoviruses, which might be used for biological control to invasion by more aggressive strains of the fungus. To this endthe viral genome was cloned and sequenced revealing four genomic segments, each one containing a single open reading frame (ORF) flanked by 5’ and 3’ untranslated regions. The ORFs encode the RNA-dependent RNA polymerase, the capsid protein, a protein of unknown function and a putative protease, respectively. Phylogenetic analysis of the sequences obtained revealed their similarity to members of the established family Chrysoviridae, genus Alphachrysovirus, which are encapsidated in isometric particles and are known to elicit hypovirulence in their hosts. Subsequently, virus-free and virus-infected isogenic lines were generated to determine any effects of the mycovirus on fungal fitness and pathogenicity. More specifically, the virus-infected isolate is currently being assessed in comparison to the virus-free one in terms of radial growth in solid culture, biomass in liquid culture, pathogenicity in pine trees and production of the mycotoxin dothistromin. In conclusion, this study reports the first mycovirus ever found in D. septosporum.

Analysis of the novel role of NS5A domain I in the assembly of infectious hepatitis C virus particles

Hepatitis C virus (HCV) is an enveloped virus with a positive-sense, single-stranded RNA of approximately 9.6 kb, a member of the genus Hepaci virus within the family Flaviviridae. The genome contains a single large open reading frame encoding a 3000 residue polyprotein. The non-structural 5A protein (NS5A) is a highly phosphorylated protein, whichis comprised of three domains (I, II and III). Previously, we demonstrated that two residues within NS5A domain I (V67 and P145) play critical roles in HCV assembly challenging the dogma that NS5A domain I exclusively participated in genome replication. In this study, we identified 8 surface exposed residues of domain Iwhich were located in close proximity to V67 and P145. The mutants were cloned into a JFH-1 derived subgenomic replicons (mSGR-luc-JFH1) to confirm whether they are required in genome replication. The results of luciferase assay suggested that I52A exhibited the same phenotype as V67A and P145A and is a further candidate for regulating assembly of HCV. In parallel we sought to investigate whether domain I was involved in the interaction of NS5A with cyclophilin A (CypA), a cellular peptidyl-prolyl isomerase required for HCV replication. CypA can be inhibited by cyclosporin A (CsA), which also inhibits HCV genome replication. Surprisingly, all three mutant replicons (I52A, V67A and P145A) were more sensitive to CsA treatment than wildtype, suggesting that domain I does indeed interact with CypA. Ongoing studies will therefore investigate the roles of both domain I and CypA in genome replication and assembly of infectious HCV particles.

Mycovirus induced hypervirulence of Leptosphaeria biglobosa enhances systemic acquired resistance to Leptosphaeria maculans in Brassica napus

Phoma stem canker is one of the most important diseases of winter oil seed rape (Brassica napus) world-wide and is caused by a complex that comprises at least two species: Leptosphaeria maculans and Leptosphaeria biglobosa. Screening a panel of field Leptosphaeria isolates from B. napus for the presence of mycoviruses revealed the presence of a novel double stranded (ds) RNA virus in L. biglobosa and no viruses in L. maculans. The virus forms isometric particles ca. 40–45 nm in diameter and has four genomic segments, each possessing a single open reading frame flanked by untranslated regions. Phylogenetic analysis revealed modest similarities to known and suspected members of the family Quadriviridaeand therefore the virus was nominated Leptosphaeria biglobosa quadrivirus-1. Following eradication of the mycovirus, virus-infected and virus-free isogenic lines of L. biglobosa were created. A direct comparison of the growth and virulence of these isogenic lines illustrated that virus infection caused hypervirulence and resulted in induced systemic resistance towards L. maculans in B. napus following lower leaf pre-inoculation with the virus-infected isolate. Analysis of the plant transcriptome suggests that the presence of the virus leads to subtle alterations in metabolism and plant defences. For instance, transcripts involved in carbohydrate and amino acid metabolism are enriched in plants treated with the virus-infected isolate, while pathogenesis-related proteins, chitinases and WRKY transcription factors are differentially expressed. These results illustrate the potential for deliberate inoculation of plants with hypervirulent L. biglobosa to decrease the severity of phoma stem canker later in the growing season.

Isolation and characterization of a novel mycovirus infecting an edible mushroom, Grifola frondosa

Abstract Grifola frondosa (Maitake mushroom) is an important cultivated mushroom due to its medicinal and nutrient values. In this study, we isolated and characterized a novel partitivirus (named Grifola frondosa partitivirus 1, GfPV1) infecting a standard G. frondosa strain Gf-N2. This virus has a two-segmented dsRNA genome (dsRNA1 and dsRNA2) with nucleotide lengths of 2.3 and 2.2 kbp, respectively. The coding strand of dsRNA1 and dsRNA2 segments carries single open reading frame encoding RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. BLAST searches and phylogenetic analyses showed that GfPV1 is most closely related to a betapartitivirus, Lentinula edodes partitivirus 1 (RdRp

Genetic variability and molecular evolution of Bean common mosaic virus populations in Iran: comparison with the populations in the world

Bean common mosaic virus (BCMV) is an important plant pathogen causing considerable economic loss to legume production worldwide. In this study, the molecular characterizations of four BCMV isolates from Iran were determined, and their genetic variation and phylogenetic relationship compared with those of 49 other from GenBank. The genome contained a single open reading frame encoding a polyprotein of 3221, 3222, 3201 and 3202 amino acids (aa) in Ir-MSC1, Ir-GoB, Ir-MJB, and Ir-MSC2, respectively. Phylogenetic analysis of the polyprotein nucleotide sequences revealed that all 53 BCMV isolates clustered into six phylogroups distinguishable according to their genetic distances, namely S (soybean), P (peanut), C (common bean) and also three other distinct groups (R1, R2, and R3) of isolates all of which were recombinant. Iranian BCMV isolates did not form a compact group in the phylogenetic trees and shared 82.7–97.0% nt and 98.6–98.9% aa sequence identity among themselves and 80.1–98.7% nt and 83.4–99.8% aa sequence identity with the 49 other BCMV isolates. Of the 53 BCMV isolates studied, 34 (including Ir-MSC1 and Ir-GoB) were found to be recombinants at multiple regions of the genomes. The 19 non-recombinant isolates fell into three main phylogroups (S, P, and C) and tended to be classified according to their original host (with some exceptions). Statistically highly significant genetic differentiation (FST > 0.80) and infrequent gene flow were detected between the three phylogroups, suggesting ancestral differentiation. The normalized values for dN-dS indicated different purifying selection pressures acting on each of cistrons, with the P1 and NIa-Pro being subjected to the weakest and strongest functional constraints, respectively. Some codons (mainly in P1 and P3 regions) were under positive selection. This study presents a comprehensive analysis of evolutionary forces shaping the genetic structure of BCMV with implications for international exchanges of propagating materials.

Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids.

A fundamental question in evolutionary biology is how genetic novelty arises. De novo gene birth is a recently recognized mechanism, but the evolutionary process and function of putative de novo genes remain largely obscure. With a clear life-saving function, the diverse antifreeze proteins of polar fishes are exemplary adaptive innovations and models for investigating new gene evolution. Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence. We constructed genomic DNA libraries for AFGP-bearing and AFGP-lacking species across the gadid phylogeny and performed fine-scale comparative analyses of the AFGP genomic loci and homologs. We identified the noncoding founder region and a nine-nucleotide (9-nt) element therein that supplied the codons for one Thr-Ala-Ala unit from which the extant repetitive AFGP-coding sequence (cds) arose through tandem duplications. The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal. Through a 1-nt frameshift mutation, these two parts formed a single read-through open reading frame (ORF). It became functionalized when a putative translocation event conferred the essential cis promoter for transcriptional initiation. We experimentally proved that all genic components of the extant gadid AFGP originated from entirely nongenic DNA. The gadid AFGP evolutionary process also represents a rare example of the proto-ORF model of de novo gene birth where a fully formed ORF existed before the regulatory element to activate transcription was acquired.

Characterization of a novel RNA virus from the phytopathogenic fungus Leptosphaeria biglobosa related to members of the genus Mitovirus

Mycovirus infection is a universal phenomenon in the major fungus groups. So far, however, mycoviruses have not been described in the phytopathogenic fungus Leptosphaeria biglobosa, the causal agent of phoma stem canker (blackleg). Here, we report the complete genome sequence of a novel mitovirus, Leptosphaeria biglobosa mitovirus 1 (LbMV1), isolated from the strain H3-38 of L. biglobosa. The LbMV1 genome comprises 2568 nucleotides with a low G+C content of 30%. Using the mitochondrial genetic code, the genome of LbMV1 was found to contain a single large open reading frame that encodes a predicted protein of 756 amino acids. Multiple alignment of the predicted protein sequence showed the highest similarity (51% identity) to the putative RNA-dependent RNA polymerase of Ophiostoma mitovirus 4. In addition, phylogenetic analysis grouped LbMV1 within the genus Mitovirus of the family Narnaviridae. Our results suggest that the double-stranded RNA found in strain H3-38 is the replicating genome of the mitovirus LbMV1, its deletion represents the first evidence of a mycovirus infecting L. biglobosa.

Endornaviruses: persistent dsRNA viruses with symbiotic properties in diverse eukaryotes.

Endornaviruses are unique, persistent, double-stranded RNA (dsRNA) viruses with symbiotic properties that infect diverse eukaryotes, such as plants, fungi, and oomycetes. Endornaviruses contain a linear dsRNA genome of approximately 10 to 17 kbp in length and are classified in the family Endornaviridae, which consists of two genera, Alphaendornavirus and Betaendornavirus. The endornaviruses encode a single long open reading frame encoding approximately 3200 to 5800 amino acid residues of conserved viral RNA helicase and RNA-dependent RNA polymerase domains, and some endornaviruses contain a site-specific nick in the coding strand of their dsRNA genome. Acute plant viruses propagate rapidly and systemically, eventually killing the host plant, and are then transmitted horizontally. In contrast, plant endornaviruses have several common persistent (symbiotic) properties: a stable low copy number in the host plant, no obvious effect on the host plant, and efficient vertical transmission via gametes. Plant endornaviruses are likely maintained within host plants for hundreds of generations, so the host must stringently regulate their propagation. Whereas RNA silencing functions as a defense system against acute viruses in plants, it may be necessary for the persistent infection (symbiotic life cycle) of endornaviruses. This process includes the stringent regulation of low virus copy number (steady replication before every host cell division) and efficient vertical transmission of the virus to the next generation.

Genetic diversity of the Yokose virus, XYBX1332, isolated from bats (Myotis daubentonii) in China

BackgroundYokose virus was first isolated from bats (Miniopterus fuliginosus) collected in Yokosuka, Japan, in 1971, and is a new member of the family Flaviviridae, genus Flavivirus. In this study, we isolated a Yokose virus from a serum sample of Myotis daubentonii (order Chiroptera, family Vespertilionidae) collected in Yunnan province, China in 2013.MethodsThe serum specimens of bat were used to inoculate in BHK-21 and Vero E6 cells for virus isolation. Then the viral complete genome sequence was obtained and was used for phylogenetic analysis performed by BEAST software package.ResultsThe virus was shown to have cytopathic effects in mammalian cells (BHK-21 and Vero E6). Genome sequencing indicated that it has a single open reading frame (ORF), with a genome of 10,785 nucleotides in total. Phylogenetic analysis of the viral genome suggests that XYBX1332 is a Yokose virus (YOKV) of the genus Flavivirus. Nucleotide and amino acid homology levels of the ORF of XYBX1332 and Oita-36, the original strain of YOKV, were 72 and 82%, respectively. The ORFs of XYBX1332 and Oita-36 encode 3422 and 3425 amino acids, respectively. In addition, the non-coding regions (5′- and 3′-untranslated regions [UTRs]) of these two strains differ in length and the homology of the 5′- and 3′-UTRs was 81.5 and 78.3%, respectively.ConclusionThe isolation of YOKV (XYBX1332) from inland China thousands of kilometers from Yokosuka, Japan, suggests that the geographical distribution of YOKV is not limited to the islands of Japan and that it can also exist in the inland areas of Asia. However, there are large differences between the Chinese and Japanese YOKV strains in viral genome.

A novel putative member of the family Benyviridae is associated with soilborne wheat mosaic disease in Brazil

Soilborne wheat mosaic disease (SBWMD), originally attributed to infections by Soilborne wheat mosaic virus (SBWMV) and Wheat spindle streak mosaic virus (WSSMV), is one of the most frequent virus diseases and causes economic losses in wheat in southern Brazil. This study aimed to characterize molecularly the viral species associated with wheat plants showing mosaic symptoms in Brazil. Wheat leaves and stems displaying mosaic symptoms were collected from different wheat cultivars in Passo Fundo municipality, Rio Grande do Sul State, southern Brazil. Double‐stranded RNA was extracted and submitted to cDNA library synthesis and next‐generation sequencing. No sequences of SBWMV and WSSMV were detected but the complete genome sequence of a putative new member of the family Benyviridae was determined, for which the name wheat stripe mosaic virus (WhSMV) is proposed. WhSMV has a bipartite genome with RNA 1 and RNA 2 organization similar to that of viruses belonging to Benyviridae. WhSMV RNA 1 has a single open reading frame (ORF) encoding a polyprotein with putative viral replicase function. WhSMV RNA 2 has six ORFs encoding the coat protein, the major protein (read‐through), triple gene block movement proteins (TGB 1, 2 and 3) and ORF 6 (hypothetical protein). In addition to the genomic organization and nucleotide and amino acid sequence identities, phylogenetic analyses also corroborated that WhSMV is a virus species of the Benyviridae. However, isolates of WhSMV formed a clade distinct from members of the genus Benyvirus. It was also demonstrated that the plasmodiophorid Polymyxa graminis is associated with wheat roots showing SBWMD symptoms and infected by WhSMV.

Complete genome sequence of a novel mitovirus from the wheat stripe rust fungus Puccinia striiformis.

The complete genome of a novel mycovirus, Puccinia striiformis mitovirus 1 (PsMV1), derived from the wheat stripe rust fungus Puccinia striiformis strain SCSN-10, was sequenced and analyzed. The full-length cDNA sequence is 2496bp in length with a predicted AU content of 57.65% in the genomic RNA. Sequence analysis indicated that a single large open reading frame (ORF) is present on the positive strand when the fungal mitochondrial genetic code is used. The single ORF encodes a putative RNA-dependent RNA polymerase of 743 amino acids with a molecular mass of 84.9kDa that shares the closest similarity with the corresponding proteins of Cronartium ribicola mitovirus 5 and Helicobasidium mompa mitovirus 1-18 (34% and 35% aa sequence identity, respectively). Phylogenetic analysis further indicated that PsMV1 is a new member of the genus Mitovirus within the family Narnaviridae. This is the first report of the full-length nucleotide sequence of a novel mitovirus, PsMV1, from the causal agent of wheat stripe rust.

A novel chrysovirus from a clinical isolate of Aspergillus thermomutatus affects sporulation.

A clinical isolate of Aspergillus thermomutatus (Teleomorph: Neosartorya pseudofischeri) was found to contain ~35 nm isometric virus-like particles associated with four double-stranded (ds) RNA segments, each of which coded for a single open reading frame. The longest dsRNA element (3589 nt) encodes a putative RNA-dependent RNA polymerase (1114 aa), the second longest dsRNA element (2772 nt) encodes a coat protein (825 aa), and the other two dsRNAs (2676 nt, 2514 nt) encode hypothetical proteins of 768 aa and 711 aa, respectively. Phylogenetic analysis of the amino acid sequences showed 41–60% similarity to the proteins coded by the dsRNAs of the most closely related virus, Penicillium janczewskii chrysovirus 2, indicating that it is a new species based on the International Committee on Taxonomy of Viruses criteria for the genus Chrysovirus. This is the first virus reported from A. thermomutatus and was tentatively named Aspergillus thermomutatus chrysovirus 1. A virus free line of the fungal isolate, cured by cycloheximide treatment, produced large numbers of conidia but no ascospores at both 20°C and 37°C, whereas the virus infected line produced ten-fold fewer conidia at 20°C and a large number of ascospores at both temperatures. The effects of the virus on fungal sporulation have interesting implications for the spread of the fungus and possible use of the virus as a biological control agent.

First report of a novel alphapartitivirus in the basidiomycete Rhizoctonia oryzae-sativae.

Rhizoctonia oryzae-sativae is a soil-borne basidiomycete fungus that causes aggregate sheath spot disease on rice worldwide. Here, we report the complete genome sequence of a partitivirus designated as Rhizoctonia oryzae-sativae partitivirus 1 (RosPV1) infecting this fungus. The genome of RosPV1 consists of two double-stranded RNA(dsRNA) segments. The larger segment, designated as dsRNA-1 (1,961 bp), contains a single open reading frame (ORF) that encodes a putative polypeptide with a conserved RNA-dependent RNA polymerase (RdRp) domain. The smaller segment, dsRNA-2 (1,819bp), also has a single ORF, which is predicted to encode the capsid protein (CP). BLAST searches and phylogenetic analyses suggested that RosPV1 is a representative member of a new species within the genus Alphapartitivirus. This is the first report of an alphapartitivirus infecting the fungus R. oryzae-sativae.

The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis.

The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.